linking problem with modified DNA base
- Dear all,
I am refining a crystal structure with a modified DNA base. I tried to
input the modification via a patch in cns (1.2). So, I modified
generate.inp, dna-rna.top, dna-rna.param and dna-rna.link accordingly
(see below). When I generate pdb/mtf files and refine in cns I do not
get any errors in the logs. However, all residues of the DNA have broken
bonds between P and O3' (distance is 1.8 instead of 1.6 A; everywhere
not only where the modified base is). Can anybody point me to settings I
can check or things I might have overlooked? Is the link definition correct?
Of course, I am also trying to define the modification with a
non-standard residue but a patch would be the easiest solution for my case.
>> in generate.inp:patch PCH
reference=1=(segid A and resid 6)
reference=2=(segid A and resid 7)
>> in dna-rna.top:PRESidue PCH
MODIFY ATOM ... TYPE=... END
ADD BOND ...
ADD ANGLe ...
ADD DIHEdral ...
ADD IMPRoper ...
>> in dna-rna.parambond ...
>> in dna-rna.link:link nuc head - pch tail + * end
link pch head - nuc tail + * end
Dr. Christian Biertümpfel
Laboratory of Molecular Biology
NIDDK/National Institutes of Health phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201
Bethesda, MD 20892-0580